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CHECK report for epihet on malbec1

This page was generated on 2021-05-06 12:27:29 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the epihet package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 557/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
epihet 1.6.1  (landing page)
Xiaowen Chen
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/epihet
Branch: RELEASE_3_12
Last Commit: 9cff2f9
Last Changed Date: 2020-12-21 10:26:58 -0400 (Mon, 21 Dec 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: epihet
Version: 1.6.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:epihet.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings epihet_1.6.1.tar.gz
StartedAt: 2021-05-06 01:19:09 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:22:44 -0400 (Thu, 06 May 2021)
EllapsedTime: 214.3 seconds
RetCode: 0
Status:   OK  
CheckDir: epihet.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:epihet.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings epihet_1.6.1.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/epihet.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘epihet/DESCRIPTION’ ... OK
* this is package ‘epihet’ version ‘1.6.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'GenomicRanges', 'IRanges', 'S4Vectors', 'ggplot2', 'foreach',
  'Rtsne', 'igraph'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘epihet’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
epiPathway 12.34    0.1   13.68
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/epihet.Rcheck/00check.log’
for details.



Installation output

epihet.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL epihet
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘epihet’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (epihet)

Tests output


Example timings

epihet.Rcheck/epihet-Ex.timings

nameusersystemelapsed
compMatrix0.3680.0120.383
epiBox0.0280.0000.030
epiMA0.0080.0000.006
epiMap0.0720.0000.070
epiPCA0.4000.0000.693
epiPathway12.34 0.1013.68
epiTSNE0.2520.0000.251
jaccard0.0040.0040.009
makeGR0.1600.1800.615
moduleAnno0.2040.0200.224
moduleSim0.0360.0000.036
moduleVisual0.1440.0200.163
readGR0.0240.0320.060
shannon0.0040.0000.000
splitn000
summarize0.0920.0120.106
userobj0.0200.0040.028